wiki:net.sf.basedb.meludi.notes1_3_3

Updating to MeLuDI 1.3.3

Same procedure as last year ... well, at least as release 1.3.2. Since the wizard "Update processed start lists with lot numbers from extracts" was found to often fail to successfully update an older start item list with new lot numbers, it is necessary to perform that procedure again, using the updated version of the wizard in MeLuDI 1.3.3. For simplicity, the full instructions are repeated below, updated with current version numbers:

Updating to MeLuDI 1.3.3 might require some manual changes for items that already exist. This is due to the following decision (See ticket:802 and ticket:815 for more information):

  • Starting with MeLuDI 1.3.2, input of all lot numbers of interest is performed in the first DNA/RNA extraction wizard, the "Lab tracking protocol for FFPE extraction" wizard, and the entered lot numbers are stored with the created start item list. Other DNA/RNA extraction wizards obtain the default lot numbers from the input start item list. (Previously, most lot numbers for processed start item lists were obtained from the first DNA extract on the list.)

Consequences for older start item lists:

  • Previously, the lot number for the "FFPE DNA/RNA kit" entered in the first extraction wizard was stored as annotation for the created start item list, while all other lot numbers were entered in the following DNA/RNA registration wizard and stored as annotations for the created DNA/RNA extract items. Since individual entries for extracts were allowed, and still are, it was found better to store default lot numbers as annotations to the start item list. In order for the updated "Lab tracking protocol/report copy" wizard to be able to display all lot numbers for start item lists created prior to MeLuDI v1.3.2, the latter start lists need to be updated.

Wizard "Update processed start lists with lot numbers from extracts" has been added to the "Special conversion tools" sub-section of the "Admin" section. It allows a number of processed start item lists to be selected from a menu (normally all start item lists are selected, if the conversion is performed directly after installing MeLuDI v1.3.3). For each selected start item list, new lot number annotations of the latter will be set to values of the corresponding annotations for the first DNA extract, or if no such extract exists, the first RNA extract (MeLuDI items are used if existing, otherwise extra material items). The new extraction operator annotation will not be set, as it was not defined for extracts prior to MeLuDI v1.3.2. The conversion tool is only needed once, after update to MeLuDI v1.3.3, and can therefore be removed in later versions.

Older unprocessed start item lists do not state a problem, even though they lack values for most lot numbers, since these will be added in the "DNA/RNA registration/quantification" wizard.

Follow this procedure:

1. Preparations before update to MeLuDI v1.3.3

  1. MeLuDI v1.3.3 requires at least version 3.5.0 of BASE. If needed, update BASE before installing MeLuDI v1.3.3.
  2. MeLuDI v1.3.3 has been tested successfully with Tomcat 8, but should still work with Tomcat 7.

2. Update to MeLuDI v1.3.3

Among other things, annotation types for all lot numbers are installed for item lists.

  1. After installation of MeLuDI v1.3.3, run the installation wizard.

3. Update processed start lists with lot numbers from extracts

In section "Server administrator wizards" of the MeLuDI v.1.3.3 software, select the "Update processed start lists with lot numbers from extracts" wizard.

  1. Select the processed start item lists you want to update (normally all the start lists).
  2. Click "Register" to update the start lists.

Each selected processed start list will be updated as follows:

  1. New start list lot number annotations will be set to values of the corresponding annotations for the first DNA extract.
  2. The new extraction operator annotation will not be set, as it was not defined for extracts prior to MeLuDI v1.3.3.

The updated start lists can now be checked in the "Lab tracking protocol/report copy" wizard.

Last modified 2 years ago Last modified on Oct 1, 2015, 4:00:14 PM